
/*
    bio_molecular.h: Molecular Biology ++ Header file.
    Copyright (C) 2012 Hugo Arregui, FuDePAN

    This file is part of Biopp.

    Aso is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    Biopp is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with Biopp.  If not, see <http://www.gnu.org/licenses/>.

    NOTE: This file is in prototype stage, and is under active development.
*/

#ifndef BIOMOLECULAR_DEFINITIONS_H
#define BIOMOLECULAR_DEFINITIONS_H

#include "bio_alphabet.h"
#include "biopp_iterators.h"

namespace biopp
{

typedef Aminoacid_Alphabet<> Aminoacid;
typedef AXCG_Alphabet<> Nucleotide;
typedef Pseudo_Alphabet<AXCG_Alphabet<> > PseudoNucleotide;

class Triplet;

typedef IteratorInterface<Triplet> TripletsIteratorInterface;
typedef IteratorInterface<Aminoacid> AminoacidsIteratorInterface;
typedef Iterator<Triplet> TripletsIterator;
typedef Iterator<Aminoacid> AminoacidsIterator;

typedef float NucDistance;

#define MATRIX_SIZE 4
typedef NucDistance DistanceMatrix[MATRIX_SIZE][MATRIX_SIZE];

}

#endif
